Re: [gmx-users] how to write .top file for a rigid molecule
Dear Jinyao, If you are talking about making the ring rigid and side group rigid, I would suggest adding a bunch of improper dihedrals to keep the molecule rigid. I found without adding the improper dihedrals that molecules that I would expect to be rigid were uncharacteristically conformationally flexible. I hope that helps. Best wishes, Art Roberts University of Washington On Nov 11, 2008, at 7:25 PM, Jinyao Wang wrote: gmx-users, I am goning to carry out a rigid system system simulation for Benzaldehyde. Atom charges,Bonds and Angles come from Gaussion03 computation. LJ interaction parameters come from oplsaa forcefield. I don't know how to deal with rigid molecules in gromacs. So I couldnot know how to write the .top file for the rigid Benzaldehyde. If you could give me some suggest, It is appreciated. Jinyao Wang [EMAIL PROTECTED] 2008-11-12 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .top file
hello everyone, while doing grompp for prest by giving command grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o *_md_water_prest.tpr *i get the error* -- Program grompp, VERSION 4.0 Source code file: toppush.c, line: 1196 Fatal error: [ file posre.itp, line 8 ]: Atom index (7) in position_restraints out of bounds (1-3). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. *my topology file is * ; The Force Fields to be included #include ffgmx.itp ; Include topology #include boc.itp *; Include water topology #include spc.itp ; Include position restraint file #ifdef POSRES #include posre.itp #endif* #ifdef POSRE_WATER ; Position Restraint for each water oxygen [ position_restraints ] ; i functfcx fcyfcz 1 1 1000 1000 1000 #endif [ system ] ; Name DRG in water [ molecules ] ; Compound#mols DRG 1 *but then on ur advice to the mail which i had written earlier i had rearrange my top file i.e i had interchanged water topolgy and position restraint position i.e.* ; The Force Fields to be included #include ffgmx.itp ; Include topology #include boc.itp *; Include position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp * #ifdef POSRE_WATER ; Position Restraint for each water oxygen [ position_restraints ] ; i functfcx fcyfcz 1 1 1000 1000 1000 #endif [ system ] ; Name DRG in water [ molecules ] ; Compound#mols DRG 1 SOL 936 *After that i get no error. tell me whether i m correct at this point * Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] position restrain
Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 Scaling Benchmarks...
Am Mittwoch 12 November 2008 06:18:14 schrieb vivek sharma: Everybody thanks for your usefull suggestions.. What do you mean by % imbalance reported in log file. I don't know how to assign the specific load to PME, but I can see that around 37% of the computation is being used by PME. I am not assigning PME nodes separately. I have no idea of dynamic load balancing and how to use it ? The switch is -dlb Normally it's turned on automatically (auto), but you can turn it on/off with this switch as well. -dds might be of interest as well... Best Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density of the bilayer
On 12 Nov 2008 11:13:51 - minnale [EMAIL PROTECTED] wrote: Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? I do not see the same values! They seem to fluctuate! What would be so wrong in having similar values? Looks good to me! the command line is g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 5ns_den.xvg/20ns_den.xvg density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4) 5ns_den.xvg 20ns_den.xvg 0 916.8650 869.8 0.113182 886.8920.114679 840.058 0.226364 840.4790.229359 793.811 0.339547 782.5090.344038 736.194 0.452729 718.7990.458717 667.985 0.565911 652.1120.573397 589.507 0.679093 576.4810.688076 509.389 0.792275 501.5020.802755 437.914 0.905457 423.9930.917435 374.713 1.01864 346.6351.03211 314.386 1.13182 266.881.14679 247.738 1.245 195.441.26147 173.424 1.35819 123.3631.37615 107.955 1.47137 68.32161.49083 51.0066 1.58455 34.01541.60551 21.3937 -- ---- -- -- ---- -- -- ---- -- any comments would be appreciated Thanks in advance - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compilation of gmx-4.0.2
Thanks Mark and Justin,
I got the script of installation of gromacs3.3.1 from the system
manager. It works so far ... I attached it at the end (note: it is for
double precision), it might help others.
The mpicc was not found as mpcc was used instead.
Best,
XAvier
script
# 32 or 64 bit version
export OBJECT_MODE=64
# C compiler
export CC='xlc_r -q64 -qsuppress=1506-229 '
export CFLAGS='-O3 -qhot -qarch=auto -qtune=auto -qmaxmem=-1'
# C++ compiler
export CXX='xlC_r -q64'
export CXXFLAGS='-O3 -qhot -qarch=auto -qtune=auto -qmaxmem=-1'
# Fortran compiler
export FC='xlf95_r -q64'
export FFLAGS='-O3 -qhot -qarch=auto -qtune=auto -qmaxmem=-1'
# MPI compilers
export MPICC='mpcc -q64 -compiler xlc_r'
export MPIF90='mpfort -q64 -compiler xlf95_r'
# LDFLAGS linker flags, e.g. -Llib dir if you have libraries in a
# nonstandard directory lib dir
# headers in a nonstandard directory include dir
# CPP C preprocessor
rootdir=$PWD
echo Rootdir: $rootdir
export MP_HOSTFILE=$rootdir/hostfile
echo $MP_HOSTFILE
cat ${MP_HOSTFILE} EOF
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
EOF
# make fftw3 available
echo Loading ffwt3 version
module load fftw3
builddir=$PWD/build-dp
mkdir -p ${builddir} || exit
cd ${dir} || exit
echo Configuring double precision mpi parallel version
echo ./configure --prefix=${builddir} --program-suffix=_mpi --without-x
--disable-float --enable-mpi
./configure --prefix=${builddir} --program-suffix=_mpi --without-x
--disable-float --enable-mpi
make mdrun
make install-mdrun
-end script-
On Wed, 12 Nov 2008 11:20:22 +1100
Mark Abraham [EMAIL PROTECTED] wrote:
Xavier Periole wrote:
Dears,
my turn to ask a stupid question:
I am trying to install gmx402 on a IBM pSeries 575
CPUs: dual core IBM Power6
when running the command:
./configure --enable-mpi --prefix==/home/X/gmx402/
I run very into the error:
.
.
checking size of int... configure: error: cannot compute sizeof (int)
See config.log for more details.
config.log did not help much.
Is this a known issue? I had never seen it.
Yep there's at least one known cause. By default, configure assumes that you
are building on the same architecture on which your target will run. So when
testing for machine properties it can use either successful compilation or
successful execution. However in a cross-compilation environment, the latter
will fail.
There are several work-arounds. There's a tool called yodconfigure that I
understand takes care of much of such issues, but I'm not sure how. Or you
can trick configure into running code on the target machine somehow - this is
tricky with GROMACS, because in src/gmxlib/nonbonded/nb_kernel you need to
make and run on the build machine to create the generic kernels. Or you can
tell configure you are cross-compiling with the --build and --host flag, so
that it uses only successful compilation as a diagnostic tool.
I'm surprised that lack of mpicc caused such a problem and didn't cause a
problem when testing mpicc.
Mark
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-
XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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Re: [gmx-users] density of the bilayer
On 12 Nov 2008 11:41:54 - minnale [EMAIL PROTECTED] wrote: Thanks for your reply, In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case starting water density itself reducing gradually instead of coming straight line for while. is my opinion wrong? Ok there you seem to be right. Do you actually do the density only on water? You should give an index to g_density and choose from it the water or something else. Is your system centered? I mean the bilayer in the center of the z axis and therefore the water distributed on both sides. Do you actually have enough water solvating your balayer and therefore showing this plateau value before the decrease? XAvier how actally I should get the water density plot of the bilayer? any suggestions would be appreciated thanks in advance On Wed, 12 Nov 2008 Xavier Periole wrote : On 12 Nov 2008 11:13:51 - minnale [EMAIL PROTECTED] wrote: Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? I do not see the same values! They seem to fluctuate! What would be so wrong in having similar values? Looks good to me! the command line is g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 5ns_den.xvg/20ns_den.xvg density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4) 5ns_den.xvg 20ns_den.xvg 0 916.8650 869.8 0.113182 886.8920.114679 840.058 0.226364 840.4790.229359 793.811 0.339547 782.5090.344038 736.194 0.452729 718.7990.458717 667.985 0.565911 652.1120.573397 589.507 0.679093 576.4810.688076 509.389 0.792275 501.5020.802755 437.914 0.905457 423.9930.917435 374.713 1.01864 346.6351.03211 314.386 1.13182 266.881.14679 247.738 1.245 195.441.26147 173.424 1.35819 123.3631.37615 107.955 1.47137 68.32161.49083 51.0066 1.58455 34.01541.60551 21.3937 -- ---- -- -- ---- -- -- ---- -- any comments would be appreciated Thanks in advance - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] GROMACS on Bluegene
Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on Bluegene Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] small protein big frozen group - exploding
Dear, I am simulating a small protein (less then 50 amino acids) at room temperature, with no additional atoms and/or molecules and/or ions. The simulations seems to proceed ok (in terms of avg. kinetic energy and other energy terms). Then, I take the same protein, and introduce a surface to the system. My surface is just a set of identical hard sphere atoms, here is how a surface atom is defined inside my .TOP file: [ atomtypes ] ;name mass charge ptype c6 c12 X 1.0000.000 X0.000 0.600E-09 And there are 10 times more surface atoms then protein atoms. In my .MDP file, there are two energy groups: protein non-protein. The surface is frozen in all xyz directions. Now, the problem is that with the surface, my protein quickly explodes, and I have no idea why. The surface and protein each coupled to its own thermostat. Your help and ideas/comments are appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force Fields for Solids
Hi, I read that some have been using GROMACS to model epoxy polymers, and I'm wondering which force field you've been using. I'd ideally like to implement the new DFTB+ code into GROMACS to run some QM/MM simulations of epoxy/TiO2 nanocomposites. Thanks, Chris Rowan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] density of the bilayer
Thanks for your reply, In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case starting water density itself reducing gradually instead of coming straight line for while. is my opinion wrong? how actally I should get the water density plot of the bilayer? any suggestions would be appreciated thanks in advance On Wed, 12 Nov 2008 Xavier Periole wrote : On 12 Nov 2008 11:13:51 - minnale [EMAIL PROTECTED] wrote: Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? I do not see the same values! They seem to fluctuate! What would be so wrong in having similar values? Looks good to me! the command line is g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 5ns_den.xvg/20ns_den.xvg density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4) 5ns_den.xvg 20ns_den.xvg 0 916.8650 869.8 0.113182 886.8920.114679 840.058 0.226364 840.4790.229359 793.811 0.339547 782.5090.344038 736.194 0.452729 718.7990.458717 667.985 0.565911 652.1120.573397 589.507 0.679093 576.4810.688076 509.389 0.792275 501.5020.802755 437.914 0.905457 423.9930.917435 374.713 1.01864 346.6351.03211 314.386 1.13182 266.881.14679 247.738 1.245 195.441.26147 173.424 1.35819 123.3631.37615 107.955 1.47137 68.32161.49083 51.0066 1.58455 34.01541.60551 21.3937 -- ---- -- -- ---- -- -- ---- -- any comments would be appreciated Thanks in advance - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem installing FFTW
Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure: WARNING: *** Couldn't figure out how to link C and Fortran; switching to --disable- fortran. I can't figure out how to fix this problem. Any suggestion will be highly helpful. Thanks in advance Sarbani ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem installing FFTW
sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure: WARNING: *** Couldn't figure out how to link C and Fortran; switching to --disable- fortran. So using --disable-fortran doesn't work? Does compilation then fail? What compilers (and versions) are you using? -Justin I can't figure out how to fix this problem. Any suggestion will be highly helpful. Thanks in advance Sarbani Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with pulling (afm_rate is not equal to real pull-velocity)
Dear all, i have with Gromacs 3.3.3 problem with the afm-pulling (the velocity are not correct) My system consists of ureas with short alkane linkers (see picture below) +___+___+ ||| x x x x x x ||| * x are the ureas (which form hbonds), | are the linkers and _ are constraints and distance restraince (so that the molecules have a nearly constant distance). * is the REF-group and + are the PULL-groups. The initial position of the three spring was at the position of the three PULL-groups. For the pull direction i took the vector between the REF-group and the middle PULL-group (and normalized the vector). The pull-direction for the other two PULL-groups was the same (so the pulling of the three molecules should be parallel). For all springs i took the same velocity and spring constant. From the *.pdo i calculeted the distance which the springs moved, and from a plot distance against time i can calculate the velocity. And here comes the problem: the velocity should be 10E-4 nm/ps For the middle spring it was: 9.995E-5 nm/ps (here i think is a small rounding error, due to the normalisation) But for one of the outer springs it was: 7.6939E-5 nm/ps ; additionally the velocity wasn't realy constant, the fit with an polynom (2end order) was much better: 6.9173E-5 (for the linear term) and 6.4715E-10 (for the quadratic term). In a simulation with 15 parallel molecules the decrease of the pulling-velocity was even more extrem. The velocity of the outter most springs was more then 5 times small then the velocity i have writen in the *.ppa file. Has anybody an idea from what this problem arises? Thanks for answers. Thomas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv write frames to separate files
Hi, i'm trying to write each frame from the bebining time=0.0 to the end time=6000 to a separate file, but it writes only the 1frame at time 0.0: trjconv -f 1ktz_p1_em.gro -s 1ktz_p1_em.tpr -o 1ktz_0.pdb -b 0.0 -e 6000.0 -sep Reading frames from gro file 'GROningen MAchine for Chemical Simulation', 1148 atoms. Reading frame 0 time0.000 Precision of 1ktz_p1_em.gro is 0.001 (nm) Last frame 0 time0.000 i guess i should provide index.ndx of frames.ndx. i havn't found anithing about what to write in these files and in what format. Tania ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv write frames to separate files
tatsiana kirys wrote: Hi, i'm trying to write each frame from the bebining time=0.0 to the end time=6000 to a separate file, but it writes only the 1frame at time 0.0: trjconv -f 1ktz_p1_em.gro -s 1ktz_p1_em.tpr -o 1ktz_0.pdb -b 0.0 -e 6000.0 -sep Reading frames from gro file 'GROningen MAchine for Chemical Simulation', 1148 atoms. Reading frame 0 time0.000 Precision of 1ktz_p1_em.gro is 0.001 (nm) Last frame 0 time0.000 What does gmxcheck tell you about the .gro file? It likely does not contain 6000 ps worth of data. i guess i should provide index.ndx of frames.ndx. i havn't found anithing about what to write in these files and in what format. They're not necessary for what you're trying to do. -Justin Tania ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
I am interested in this as well, since I am planning to compile version 4.0.2 in Blue Gene within a few days (once I get hold of my account!). -- Suman Chakrabarty. On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby [EMAIL PROTECTED] wrote: Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on Bluegene Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restrain
shahrbanoo karbalaee wrote: Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? pcoupl = yes doesn't do anything. You have to specify the type of pressure coupling (grompp should tell you that). For a discussion of the differences of NVT and NPT (and statistical ensembles in general), do some background reading on statistical mechanics and thermodynamics. It is hard to say ad hoc whether or not NPT conditions will change your data. -Justin best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] density of the bilayer
Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? the command line is g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 5ns_den.xvg/20ns_den.xvg density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4) 5ns_den.xvg 20ns_den.xvg 0 916.8650 869.8 0.113182 886.8920.114679 840.058 0.226364 840.4790.229359 793.811 0.339547 782.5090.344038 736.194 0.452729 718.7990.458717 667.985 0.565911 652.1120.573397 589.507 0.679093 576.4810.688076 509.389 0.792275 501.5020.802755 437.914 0.905457 423.9930.917435 374.713 1.01864 346.6351.03211 314.386 1.13182 266.881.14679 247.738 1.245 195.441.26147 173.424 1.35819 123.3631.37615 107.955 1.47137 68.32161.49083 51.0066 1.58455 34.01541.60551 21.3937 -- ---- -- -- ---- -- -- ---- -- any comments would be appreciated Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:density of the bilayer
Thanks alot for your reply In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case starting water density itself reducing gradually instead of coming straight line for while. is my opinion wrong? Ok there you seem to be right. Do you actually do the density only on water? You should give an index to g_density and choose from it the water or something else. I have calculated density for all groups seperately like phosphate, choline etc. but every group is fine except water density that's why I posted question to archives. Is your system centered? I mean the bilayer in the center of the z axis and therefore the water distributed on both sides. How can we know that system is centered or not? Do you actually have enough water solvating your balayer and therefore showing this plateau value before the decrease? I have taken popc structure form Dr.Tieleman's site and simulating contain 2460 water molecules sorry for the asking trivial queries I am new to bilayer simulations Any suggestions would be appreciated Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Warning in compiling GMX4.0.2
On Wed, 12 Nov 2008 11:48:11 +0100 Xavier Periole [EMAIL PROTECTED] wrote: Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Should that be a worry? Note that the warning disappeared with the option -qaltivec added to the CFLAGS and CXXFLAGS. Well it did not appear as much so I actually missed it! It does still appear occasionally. XAvier. - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: grompp NOTE mdp file concerning steps
Hello, searching further the issue, I realized that no more than 32299167 number of steps can be used. In case someone uses more, the note I describe makes its appearance. Is this a new limit? Regards, Nikos --- Claus Valka [EMAIL PROTECTED] schrieb am Mi, 12.11.2008: Von: Claus Valka [EMAIL PROTECTED] Betreff: grompp NOTE mdp file concerning steps An: gmx-users@gromacs.org Datum: Mittwoch, 12. November 2008, 12:29 Hello, I'm using gromacs version 4.0 and when I type : grompp -f file.mdp -c file.gro -p topol.top I get this note: NOTE 1 [file file.mdp, line unknown]: and nothing else. I checked my mdp file and I noticed than when I give 5000 steps I get this error (steps with more than 7 digits). If e.g. I give 500 steps I do not get this message. Testing it with previous versions I do not get this note-error. Am I the only one facing this? Should I pay attention or is something trivial? Regards, Nikos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Versions of analysis programs
Hi, I've noticed that the VERSION entry of the analysis programs in GMX 4.0.2 is 3.2.0 or 3.3.2, whereas in GMX 3.3.3 it's 3.3.3. Is that just a typo? Thanks, Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Warning in compiling GMX4.0.2
Mark Abraham wrote: Xavier Periole wrote: Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Should that be a worry? Depending on the architecture, different optimizations get added in as -Ox gets higher. You can selectively add higher things, e.g. -qhot, which is probably a default at -O4. You should start with the compiler man page to get some idea what this might affect. More exhaustive PDF documentation does accompany all of the IBM compilers. Often you can find it in installed in a subdirectory near where the compiler is found in your path. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Warning in compiling GMX4.0.2
Xavier Periole wrote: Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Should that be a worry? Depending on the architecture, different optimizations get added in as -Ox gets higher. You can selectively add higher things, e.g. -qhot, which is probably a default at -O4. You should start with the compiler man page to get some idea what this might affect. Look for -qstrict to see what optimizations might be involved here. For example, there are some floating-point optimizations, particularly involving reciprocals or reciprocal square-roots, that only produce approximate results. One might or might not want to use these, hence the warning. Other optimizations might enable the compiler to not check for underflows, division by zero or other such maths-fails. All these kind of things can mean that the optimized code produces a different result from non-optimized. Roughly speaking, I'd say it's not a worry for GROMACS. Note that the warning disappeared with the option -qaltivec added to the CFLAGS and CXXFLAGS. That probably just means that the bit that was causing the warning to be issued is now being vectorized, e.g. a reciprocal square-root. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Is it normal for mdrun to go very slow when a large number of 'energygrps' user-defined potentials are used? (This re-post is easier to read)
Dear GROMACS users, I am hoping to get some information from you experts regarding the use of user-defined potentials (table*.xvg). With the help of the GROMACS manual and several posts in the mailing list, I have been able to make user-defined potential functions that I would like to apply to a system of small molecules (16 atoms each, ~100 molecules). The crux of the problem (see below) is that I would like to apply **separate** user-defined potentials for *intra* and *inter* molecular interactions **in a computationally efficient way**. The molecule I'm simulating (in united-atom representation) is: C1 - O1 - C - C - O2 - C2 and I want: (1) a user defined potential applied between C1 and C2 on the same molecule (2) a different user defined potential between C2 and O1 ( C1 and O2) on the same molecule (3) a normal gromacs table potential applied between C1 and C2 on *different* molecules (4) a normal gromacs table potential applied between C2 and O1 (also C1 and O2) on *different* molecules I can do this by defining a large number of 'energygrps'; specifically I need 4 different 'energygrps' for each molecule (i.e. separate ones for 'C1', 'C2', 'O1', 'O2', with all other atoms lumped into a single 'energygrp' for all molecules). Because my simulation system currently contains 91 molecules this results in 365 'energygrps' in the *.mdp file. Since this is a lot of 'energygrps' I redimensioned the gromacs arrays in order to handle it as noted previously in the mailing list: http://www.gromacs.org/pipermail/gmx-users/2007-October/030084.html This works great but **here's the problem** : the simulations run exceedingly slow when I use such a high number of defined 'energygrps'. Without using the user defined potential functions I was getting roughly 25 ns/day (which, as always with GROMACS, is amazingly fast!). With the applied potential functions and 'energygrps' however I am only getting 1.5 ns/day. I thought one problem might be the number of times that 'mdrun' spends writing to the energy (.edr) file, but I have ruled this out as a possibility because when I increased my 'nstenergy' in my *.mdp file by 100 fold 'mdrun' still runs at the same slow rate. The slowdown therefore appears to be directly related to the number of 'energygrps.'. To confirm this, I decreased the number of 'energygrps' to 3 (by lumping all 'C1' and 'C2' atoms together into one 'energygrp' and all 'O1' and 'O2' atoms into another 'energygrp') and this accelerated the simulations dramatically; however, the same user defined potential functions are then applied to both **intra** and **inter**molecular interactions, which is not what I want! If anyone has any suggestions for speeding up the simulations I'd really appreciate hearing from you! Thanks in advance for your help. Any and all comments are appreciated :) Eli Musselman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
Mathias has updated the wiki: http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene On Wed, Nov 12, 2008 at 11:57 AM, Suman Chakrabarty [EMAIL PROTECTED] wrote: I am interested in this as well, since I am planning to compile version 4.0.2 in Blue Gene within a few days (once I get hold of my account!). -- Suman Chakrabarty. On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby [EMAIL PROTECTED] wrote: Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on Bluegene Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] centre of the system: error
Hi all, I am trying to make centre of the bilayer so I used following command line trjconv -f 20nspopc.xtc -centre rect -o 20nstrjout.xtc -n water.ndx based on http://www.gromacs.org/pipermail/gmx-users/2003-June/005995.html here I selected 3 (solution) again 3 (solution) for output of the selecting group this command ran fine when I feed 20nstrjout.xtc to g_density g_density -f 20nstrjout.xtc -s em.tpr -d z -o waterden -n water.ndx Group 0 ( System) has 14036 elements Group 1 (POPC) has 6656 elements Group 2 ( SOL) has 7380 elements Group 3 ( SOL) has 7380 elements Select a group: 3 Selected 3: 'SOL' Reading frame 0 time0.000 Segmentation fault where is the mistake happening? Could anyone tell me Thanks in advance___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Is it normal for mdrun to go very slow when a large number of 'energygrps' user-defined potentials are used?
Dear GROMACS users, I am hoping to get some information from you experts regarding the use of user-defined potentials (table*.xvg). With the help of the GROMACS manual and several posts in the mailing list, I have been able to make user-defined potential functions that I would like to apply to a system of small molecules (16 atoms each, ~100 molecules). The crux of the problem (see below) is that I would like to apply **separate** user-defined potentials for *intra* and *inter* molecular interactions **in a computationally efficient way**. The molecule I'm simulating (in united-atom representation) is: C1 - O1 - C - C - O2 - C2 and I want: (1)a user defined potential applied between C1 and C2 on the same molecule (2)a different user defined potential between C2 and O1 ( C1 and O2) on the same molecule (3)a normal gromacs table potential applied between C1 and C2 on *different* molecules (4)a normal gromacs table potential applied between C2 and O1 (also C1 and O2) on *different* molecules I can do this by defining a large number of 'energygrps'; specifically I need 4 different 'energygrps' for each molecule (i.e. separate ones for 'C1', 'C2', 'O1', 'O2', with all other atoms lumped into a single 'energygrp' for all molecules). Because my simulation system currently contains 91 molecules this results in 365 'energygrps' in the *.mdp file. Since this is a lot of 'energygrps' I redimensioned the gromacs arrays in order to handle it as noted previously in the mailing list: http://www.gromacs.org/pipermail/gmx-users/2007-October/030084.html This works great but **here's the problem** : the simulations run exceedingly slow when I use such a high number of defined 'energygrps'. Without using the user defined potential functions I was getting roughly 25 ns/day (which, as always with GROMACS, is amazingly fast!). With the applied potential functions and 'energygrps' however I am only getting 1.5 ns/day. I thought one problem might be the number of times that 'mdrun' spends writing to the energy (.edr) file, but I have ruled this out as a possibility because when I increased my 'nstenergy' in my *.mdp file by 100 fold 'mdrun' still runs at the same slow rate. The slowdown therefore appears to be directly related to the number of 'energygrps.'. To confirm this, I decreased the number of 'energygrps' to 3 (by lumping all 'C1' and 'C2' atoms together into one 'energygrp' and all 'O1' and 'O2' atoms into another 'energygrp') and this accelerated the simulations dramatically; however, the same user defined potential functions are then applied to both **intra** and **inter**molecular interactions, which is not what I want! If anyone has any suggestions for speeding up the simulations I'd really appreciate hearing from you! Thanks in advance for your help. Any and all comments are appreciated :) Eli Musselman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: grompp NOTE mdp file concerning steps
Hi Nikos, You mention it raises a note. What happens to the .tpr file? Can you look for nsteps in the output from gmxdump? Cheers, Tsjerk On Wed, Nov 12, 2008 at 2:45 PM, Claus Valka [EMAIL PROTECTED] wrote: Hello, searching further the issue, I realized that no more than 32299167 number of steps can be used. In case someone uses more, the note I describe makes its appearance. Is this a new limit? Regards, Nikos --- Claus Valka [EMAIL PROTECTED] schrieb am Mi, 12.11.2008: Von: Claus Valka [EMAIL PROTECTED] Betreff: grompp NOTE mdp file concerning steps An: gmx-users@gromacs.org Datum: Mittwoch, 12. November 2008, 12:29 Hello, I'm using gromacs version 4.0 and when I type : grompp -f file.mdp -c file.gro -p topol.top I get this note: NOTE 1 [file file.mdp, line unknown]: and nothing else. I checked my mdp file and I noticed than when I give 5000 steps I get this error (steps with more than 7 digits). If e.g. I give 500 steps I do not get this message. Testing it with previous versions I do not get this note-error. Am I the only one facing this? Should I pay attention or is something trivial? Regards, Nikos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] .top file
Bhawana Gupta wrote: hello everyone, while doing grompp for prest by giving command grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o *_md_water_prest.tpr *i get the error* -- Program grompp, VERSION 4.0 Source code file: toppush.c, line: 1196 Fatal error: [ file posre.itp, line 8 ]: Atom index (7) in position_restraints out of bounds (1-3). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. *my topology file is * ; The Force Fields to be included #include ffgmx.itp ; Include topology #include boc.itp *; Include water topology #include spc.itp ; Include position restraint file #ifdef POSRES #include posre.itp #endif* #ifdef POSRE_WATER ; Position Restraint for each water oxygen [ position_restraints ] ; i functfcx fcyfcz 1 1 1000 1000 1000 #endif [ system ] ; Name DRG in water [ molecules ] ; Compound#mols DRG 1 *but then on ur advice to the mail which i had written earlier i had rearrange my top file i.e i had interchanged water topolgy and position restraint position i.e.* ; The Force Fields to be included #include ffgmx.itp ; Include topology #include boc.itp *; Include position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp * #ifdef POSRE_WATER ; Position Restraint for each water oxygen [ position_restraints ] ; i functfcx fcyfcz 1 1 1000 1000 1000 #endif [ system ] ; Name DRG in water [ molecules ] ; Compound#mols DRG 1 SOL 936 *After that i get no error. tell me whether i m correct at this point * Well, assuming the posre.itp corresponds to the molecule in boc.itp, then yes, you are correct. Position restraint files must be #included under the corresponding molecule type definition, so including it after spc.itp would mean it is being applied to water, not your molecule. Are you sure you want to be using ffgmx? It has long been considered deprecated. The Gromos96 force fields are more recent... -Justin Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp NOTE mdp file concerning steps
Hello, I'm using gromacs version 4.0 and when I type : grompp -f file.mdp -c file.gro -p topol.top I get this note: NOTE 1 [file file.mdp, line unknown]: and nothing else. I checked my mdp file and I noticed than when I give 5000 steps I get this error (steps with more than 7 digits). If e.g. I give 500 steps I do not get this message. Testing it with previous versions I do not get this note-error. Am I the only one facing this? Should I pay attention or is something trivial? Regards, Nikos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
Roland Schulz wrote: Mathias has updated the wiki: http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene That's great, there's a lot of useful info here. There are still outstanding issues with the kernels - see the discussion here and my various bugzillas http://www.gromacs.org/pipermail/gmx-developers/2008-November/002873.html Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is it normal for mdrun to go very slow when a large number of 'energygrps' user-defined potentials are used?
Musselman, Eli D wrote: This works great but ***here’s the problem*** : *the simulations run exceedingly slow when I use such a high number of defined ‘energygrps’*. Without using the user defined potential functions I was getting roughly 25 ns/day (which, as always with GROMACS, is amazingly fast!). With the applied potential functions and ‘energygrps’ however I am only getting 1.5 ns/day. I thought one problem might be the number of times that ‘mdrun’ spends writing to the energy (.edr) file, but I have ruled this out as a possibility because when I increased my ‘nstenergy’ in my *.mdp file by 100 fold ‘mdrun’ still runs at the same slow rate. The slowdown therefore appears to be directly related to the number of ‘energygrps.’. To confirm this, I decreased the number of ‘energygrps’ to 3 (by lumping all ‘C1’ and ‘C2’ atoms together into one ‘energygrp’ and all ‘O1’ and ‘O2’ atoms into another ‘energygrp’) and this accelerated the simulations dramatically; however, the same user defined potential functions are then applied to both **intra** and **inter**molecular interactions, which is not what I want! Good diagnostics and description, thanks. It seems quite likely to me that this slowdown will be related to cache misses. 95 tables actually uses an appreciable amount of memory. More salient for the inner loops, however is that each time a new table is being used in each integration step, the code will have to go and fetch locations from main memory, and when these hit the caches they won't be reused much. The only simple work-around I can suggest is to decrease the density of data points in the table. That will degrade the accuracy, but possibly lead to fewer cache misses. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Warning in compiling GMX4.0.2
Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Should that be a worry? Note that the warning disappeared with the option -qaltivec added to the CFLAGS and CXXFLAGS. XAvier. - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
Mike Hanby wrote: I keep failing the ../configure when I have -lmass or -lmassv in LIBS for the frontend gromacs configure: - checking for C compiler default output file name... configure: error: C compiler cannot create executables - XLMASS=/opt/ibmcmp/xlmass/bg/4.4 ESSL=/opt/ibmmath MPI=/bgl/BlueLight/ppcfloor/bglsys BG_INCLUDE=-I$ESSL/include -I$MPI/include -I$XLMASS/include -I$VAC/include -I$XLF/include MPILIBS=-L$MPI/lib -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts -ldevices.rts -lrts.rts ESSLLIBS=-L$ESSL/lib -lesslbg BG_LIBS=-L$VAC/lib $ESSLLIBS -lxlopt -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv $MPILIBS ../configure --prefix=$PREFIX \ --enable-fortran \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CC=xlc_r -q64 CFLAGS=-O3 -qarch=auto -qtune=auto \ CXX=xlC_r -q64 CXXFLAGS=-O3 -qarch=auto -qtune=auto \ CPPFLAGS=-I$FFTW/include $OTHERINCLUDES \ F77=xlf_r -q64 FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto \ LDFLAGS=-L$FFTW/lib \ LIBS=$XLMASS/lib -lmass -L$FFTW/lib If I remove $XLMASS/lib -lmass LIBS variable, the configure continues on. The /opt/ibmcmp/xlmass/bg/4.4 directory has the following libraries /opt/ibmcmp/xlmass/bg/4.4/bglib: libmass.a libmassv.a /opt/ibmcmp/xlmass/bg/4.4/lib: libmass.a libmassvp4.a libmassvp5.a /opt/ibmcmp/xlmass/bg/4.4/lib64: libmass_64.a libmassvp4_64.a libmassvp5_64.a Any suggestions? MASS and MASSV are some optimized math libraries with and without vectorization - anything in a bg subdirectory is only suitable for execution on the back end. Even if you have a MASS/MASSV for the front end, unless you're planning on running mdrun on it, you won't want it for 99% of GROMACS usage. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charge distribution
Hi, gmx-usrs, I want to ask for a problem on the charge distribution. I simulate the sodium dodecylbenzenesulfonate and its homologues in solution using the gromos96 force field. I can not find the similar atom type as replace in the gromos96 force field . How do I define every atomic charge? I have the mulliken charge distribution and ESP charge from the quantum calculation. Should I employ them? Can you give me some advice? Thanks a lot! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] charge distribution
Hongyan Xiao wrote: Hi, gmx-usrs, I want to ask for a problem on the charge distribution. I simulate the sodium dodecylbenzenesulfonate and its homologues in solution using the gromos96 force field. I can not find the similar atom type as replace in the gromos96 force field . How do I define every atomic charge? I have the mulliken charge distribution and ESP charge from the quantum calculation. Should I employ them? Can you give me some advice? Thanks a lot! Which atom types are unknown? Parameterization of the Gromos96 force fields relies more heavily on fitting parameters to experimental observables. Starting with QM charges isn't a bad idea, but do read the papers pertaining to the parameterization of the Gromos96 parameter sets. Free energy calculations and comparison to thermodynamic constants are necessary. -Justin H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charge distribution
Dear Justin, For sodium dodecylbenzenesulfonate(C12H25C6H4SO3Na), the charges of S and O in S03- , I cannot find the suitable charge. Forthermore, the carbon in benzene connecting the SO3- is setted to be zero, I think that there may be questionable. The polarization of SO3- is very large. what do you think so? Thanks again! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with FFTW installation
Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure: WARNING: *** Couldn't figure out how to link C and Fortran; switching to --disable- fortran. I can't figure out how to fix this problem. Any suggestion will be highly helpful. Thanks in advance Sarbani ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FFTW installation
sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure: WARNING: *** Couldn't figure out how to link C and Fortran; switching to --disable- fortran. If configure then continued on, then that's fine. FFTW is written wholly in C, it only plays with FORTRAN to work out what it needs to do to play nicely when linking with some user's FORTRAN program. I can't figure out how to fix this problem. Any suggestion will be highly helpful. Since GROMACS is written in C, this is a non-problem. Either ignore it, or use --disable-fortran like it suggests. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] problem with FFTW installation
Thank you Mark. I will continue with the installation. Sarbani On Thu, 13 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure: WARNING: *** Couldn't figure out how to link C and Fortran; switching to -- disable- fortran. If configure then continued on, then that's fine. FFTW is written wholly in C, it only plays with FORTRAN to work out what it needs to do to play nicely when linking with some user's FORTRAN program. I can't figure out how to fix this problem. Any suggestion will be highly helpful. Since GROMACS is written in C, this is a non-problem. Either ignore it, or use --disable- fortran like it suggests. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] can't find fftw3f library
Hi everybody, I am trying to install gromacs3.3.2 into my Mac Os X 10.4.1 using the source code. I have installed FFTW and the library files of fftw are in /usr/local/lib. However when I try to configure gromacs, it's gives an error : Cannot find fftw3f library. Going through the config.log file I found the following : /usr/bin/ld: can't locate file for: -lfftw3f collect2: ld returned 1 exit status I tried to specify the path to fftw library through the following: export LDFLAGS=-L/usr/local/lib, but still the problem persists. Did I understand the problem correctly? Is it right that the path to FFTW library needs to be specified correctly or is there any other problem? Any suggestion will be highly helpful. Thanks in advance Sarbani ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can't find fftw3f library
sarbani chattopadhyay wrote: Hi everybody, I am trying to install gromacs3.3.2 into my Mac Os X 10.4.1 using the source code. I have installed FFTW and the library files of fftw are in /usr/local/lib. However when I try to configure gromacs, it's gives an error : Cannot find fftw3f library. Yep. You need to configure FFTW correctly with --enable-float. See http://www.gromacs.org/content/view/23/33/ Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
